Get Bioentity from Organism
Created: 2009-09-08 15:12:57
Last updated: 2009-09-14 14:16:40
GeNS workflow that lists the identifiers corresponding to a given species and data type. For instance, list all OMIM associated with the human species.
Disclaimer: This workflow is just a simple example designed for academic purposes.
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Authors (1)
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Titles (1)
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Descriptions (1)
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Sample workflow to get all GeNS bioentities related to a given organism and data type. |
Dependencies (0)
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Inputs (2)
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Name |
Description |
Organism |
The desired Organism
|
DataType |
The desired Data Type
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Processors (19)
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Name |
Type |
Description |
SearchBioEntity |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationSearchBioEntity |
SearchBioEntityIn |
xmlsplitter |
|
SearchBioEntityOut |
xmlsplitter |
|
ListDataTypes |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationListDataTypes |
ListDataTypesIn |
xmlsplitter |
|
ListDataTypesOut |
xmlsplitter |
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SelectTaxId |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
TaxIdQuery |
stringconstant |
Value//*[local-name()="TaxonomicId"] |
SearchOrganism |
wsdl |
Wsdlhttp://bioinformatics.ua.pt/GeNS/WS/Service.asmx?wsdlWsdl OperationSearchOrganism |
SearchOrganismIn |
xmlsplitter |
|
SearchOrganismOut |
xmlsplitter |
|
SelectDataType |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
DataTypeQuery |
stringconstant |
Value//*[local-name()="DataTypeId"] |
ConcatTaxIdComma |
localworker |
Scriptoutput = string1 + string2; |
Comma |
stringconstant |
Value, |
ConcatTaxIdCommaDataType |
localworker |
Scriptoutput = string1 + string2; |
SelectAlias |
localworker |
Scriptimport org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList; |
AliasQuery |
stringconstant |
Value//*[local-name()="Alias"] |
AliasList2String |
localworker |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString();
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Beanshells (0)
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Outputs (1)
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Datalinks (22)
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Source |
Sink |
SearchBioEntityIn:output |
SearchBioEntity:parameters |
ConcatTaxIdCommaDataType:output |
SearchBioEntityIn:data |
SearchBioEntity:parameters |
SearchBioEntityOut:input |
ListDataTypesIn:output |
ListDataTypes:parameters |
DataType |
ListDataTypesIn:data |
ListDataTypes:parameters |
ListDataTypesOut:input |
TaxIdQuery:value |
SelectTaxId:xpath |
SearchOrganismOut:SearchOrganismResult |
SelectTaxId:xml-text |
SearchOrganismIn:output |
SearchOrganism:parameters |
Organism |
SearchOrganismIn:data |
SearchOrganism:parameters |
SearchOrganismOut:input |
DataTypeQuery:value |
SelectDataType:xpath |
ListDataTypesOut:ListDataTypesResult |
SelectDataType:xml-text |
SelectTaxId:nodelist |
ConcatTaxIdComma:string1 |
Comma:value |
ConcatTaxIdComma:string2 |
ConcatTaxIdComma:output |
ConcatTaxIdCommaDataType:string1 |
SelectDataType:nodelist |
ConcatTaxIdCommaDataType:string2 |
AliasQuery:value |
SelectAlias:xpath |
SearchBioEntityOut:SearchBioEntityResult |
SelectAlias:xml-text |
Comma:value |
AliasList2String:seperator |
SelectAlias:nodelist |
AliasList2String:stringlist |
AliasList2String:concatenated |
Final |
Coordinations (0)
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Sample Entity Converter
(1)
Disclaimer: This workflow is just a simple example designed for academic purposes.
Created: 2009-09-08
| Last updated: 2009-09-14
Credits:
Pedro Lopes
Search GeNS BioEntity
(1)
This workflow returns a list of know associations between an organism and a data type. All identifiers correspond to GeNS database identifiers.
Disclaimer: This workflow is just a simple example designed for academic purposes.
Created: 2009-09-15
| Last updated: 2009-09-15
Credits:
Pedro Lopes
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